Bismark report for: /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF06-EM02-Larvae_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF06-EM02-Larvae_R2_001_val_2.fq.gz (version: v0.21.0) Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cvirg-genome/ with the specified options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Option '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB) Final Alignment report ====================== Sequence pairs analysed in total: 53188835 Number of paired-end alignments with a unique best hit: 19330848 Mapping efficiency: 36.3% Sequence pairs with no alignments under any condition: 24520436 Sequence pairs did not map uniquely: 9337551 Sequence pairs which were discarded because genomic sequence could not be extracted: 7 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4734689 ((converted) top strand) GA/CT/CT: 4932868 (complementary to (converted) top strand) GA/CT/GA: 4931784 (complementary to (converted) bottom strand) CT/GA/GA: 4731500 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 615791768 Total methylated C's in CpG context: 19028347 Total methylated C's in CHG context: 2948221 Total methylated C's in CHH context: 13301236 Total methylated C's in Unknown context: 449219 Total unmethylated C's in CpG context: 72906143 Total unmethylated C's in CHG context: 127811018 Total unmethylated C's in CHH context: 379796803 Total unmethylated C's in Unknown context: 2683254 C methylated in CpG context: 20.7% C methylated in CHG context: 2.3% C methylated in CHH context: 3.4% C methylated in unknown context (CN or CHN): 14.3% Bismark completed in 0d 22h 6m 30s